Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

https://www.wwpdb.org/.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity.

Small molecule annotation for the Protein Data Bank.

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand.

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.

With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptide-like inhibitor and antibiotic molecules so that they can be easily identified and analyzed.

Crystal structure of human natural cytotoxicity receptor NKp30 and identification of its ligand binding site.

Natural killer (NK) cells are a group of innate immune cells that carry out continuous surveillance for the presence of virally infected or cancerous cells. The natural cytotoxicity receptor (NCR) NKp30 is critical for the elimination of a large group of tumor cell types. Although several ligands have been proposed for NKp30, the lack of a conserved structural feature among these ligands and their uncertain physiological relevance has contributed to confusion in the field and hampered a full understanding of the receptor.

Polygallide RE2MGa9Ge2 (RE = Ce, Sm; M = Ni, Co) phases grown in molten gallium.

The quaternary intermetallics Ce2CoGa9Ge2, Ce2NiGa9Ge2, and Sm2NiGa9Ge2 were prepared by reacting elemental metals in excess of gallium at 850 degrees C. The title compounds crystallize in the tetragonal space group P4/nmm in the Sm2Ni(Si(1-x)Ni(x))Al4Si6 structure type with cell parameters a = 5.9582(5) A, c = 15.

Structural implications of Siglec-5-mediated sialoglycan recognition.

Sialic acid (Sia) Ig-like binding lectins are important mediators of recognition and signaling events among myeloid cells. To investigate the molecular mechanism underlying sialic acid Ig-like lectin (Siglec) functions, we determined the crystal structure of the two N-terminal extracellular domains of human myeloid cell inhibitory receptor Siglec-5 (CD170) and its complexes with two sialylated carbohydrates. The native structure revealed an unusual conformation of the CC' ligand specificity loop and a unique interdomain disulfide bond.

Tb4FeGe8 grown in liquid gallium: trans-cis chains from the distortion of a planar Ge square net.

The ternary germanide Tb4FeGe8 was obtained from Ga flux reactions. The crystal structure studied with single-crystal X-ray diffraction revealed the existence of an orthorhombic average substructure (Cmcm, Z=1) with cell parameters a = 4.1118(14) A, b=15.

Intermetallics as zintl phases: Yb2Ga4Ge6 and RE3Ga4Ge6 (RE=Yb, Eu): structural response of a [Ga4Ge6]4- framework to reduction by two electrons.

Two new intermetallic compounds, Yb(2)Ga(4)Ge(6) and Yb(3)Ga(4)Ge(6), were obtained from reactions in molten Ga. A third compound, Eu(3)Ga(4)Ge(6), was produced by direct combination of the elements. The crystal structures of these compounds were studied by single-crystal X-ray diffraction.

REMGa3Ge and RE3Ni3Ga8Ge3 (M = Ni, Co; RE = rare-earth element): new intermetallics synthesized in liquid gallium. X-ray, electron, and neutron structure determination and magnetism.

New quaternary intermetallic phases REMGa(3)Ge (1) (RE = Y, Sm, Tb, Gd, Er, Tm; M = Ni, Co) and RE(3)Ni(3)Ga(8)Ge(3) (2) (RE = Sm, Gd) were obtained from exploratory reactions involving rare-earth elements (RE), transition metal (M), Ge, and excess liquid Ga the reactive solvent. The crystal structures were solved with single-crystal X-ray and electron diffraction. The crystals of 1 and 2 are tetragonal.

Isolation of the new cubic phases RE4FeGa(12-x)Ge(x) (RE = Sm, Tb; x = 2.5) from molten gallium: single-crystal neutron diffraction study of the Ga/Ge distribution.

The compounds RE4FeGa(12-x)Ge(x) (RE = Sm, Tb) were discovered in reactions employing molten Ga as a solvent at 850 degrees C. However, the isostructural Y4FeGa(12-x)Ge(x) was prepared from a direct combination reaction. The crystal structure is cubic with space group Imm, Z = 2, and a = 8.